+Open data
-Basic information
Entry | Database: PDB / ID: 4xq3 | ||||||
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Title | Crystal structure of Sso-SmAP2 | ||||||
Components | Like-Sm ribonucleoprotein core | ||||||
Keywords | RNA BINDING PROTEIN / Archael proteins | ||||||
Function / homology | Function and homology information sno(s)RNA-containing ribonucleoprotein complex / mRNA splicing, via spliceosome / viral nucleocapsid Similarity search - Function | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å | ||||||
Authors | Bezerra, G.A. / Martens, B. / Kreuter, M.J. / Grishkovskaya, I. / Manica, M. / Arkhipova, V. / Blasi, U. / Djinovic-Carugo, K. | ||||||
Citation | Journal: Life / Year: 2015 Title: The Heptameric SmAP1 and SmAP2 Proteins of the Crenarchaeon Sulfolobus Solfataricus Bind to Common and Distinct RNA Targets. Authors: Martens, B. / Bezerra, G.A. / Kreuter, M.J. / Grishkovskaya, I. / Manica, A. / Arkhipova, V. / Djinovic-Carugo, K. / Blasi, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xq3.cif.gz | 229 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xq3.ent.gz | 187.4 KB | Display | PDB format |
PDBx/mmJSON format | 4xq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/4xq3 ftp://data.pdbj.org/pub/pdb/validation_reports/xq/4xq3 | HTTPS FTP |
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-Related structure data
Related structure data | 1jriS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 10175.745 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (strain 98/2) (archaea) Strain: 98/2 / Gene: Ssol_1181 / Plasmid: pPROEX-Htb / Production host: Escherichia coli (E. coli) / Strain (production host): JW4130 deltahfq / References: UniProt: D0KRQ0 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5 Details: 0.1 M citric acid, 25% w/v polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 16, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin | Operator: h,-h-k,-l / Fraction: 0.36 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→98.607 Å / Num. all: 17319 / Num. obs: 17319 / % possible obs: 100 % / Redundancy: 5.3 % / Rpim(I) all: 0.061 / Rrim(I) all: 0.141 / Rsym value: 0.127 / Net I/av σ(I): 4.815 / Net I/σ(I): 9.2 / Num. measured all: 91134 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1jri Resolution: 2.6→49.303 Å / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 30.78 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 175.17 Å2 / Biso mean: 55.0035 Å2 / Biso min: 24.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→49.303 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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Refinement TLS params. | Method: refined / Origin x: 134.3083 Å / Origin y: 148.0233 Å / Origin z: 95.0828 Å
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Refinement TLS group |
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